Skip to content
Dabour HubLEARN · PRACTICE · EXPLORESign inStudent

7.7Advanced Organic Chemistry

Amino acids, Proteins and DNA — AQA A Level Chemistry Revision Notes & Topical Questions

5 min read 13 parts Lesson 7 of 12

📚 AQA A Level Chemistry Hub / Topical Revision
🩺
100% Curriculum Specification Match Lesson Doctor Verified
The only platform with 100% curriculum specification match and verified interactive question banks.
0%read
Lesson summary

Amino Acids, Proteins, Enzymes and Anticancer Drugs — AQA A LEVEL CHEMISTRY — COMPLETE NOTES notes: Describe the structure and acid-base behaviour of amino acids, the formation and structure of proteins, enzyme action and the action of cisplatin.Amino acids are organic compounds …

  • Worked example 1
  • Worked example 2
  • Worked example 3
  • Worked example 4
  • Zwitterion
  • Peptide link

Section 1 of 13Amino acids

Amino acids are organic compounds that contain two functional groups: an amino group (-NH2) and a carboxyl group (-COOH).

1
In the 2-amino acids found in proteins both are attached to the same carbon: H2N-CHR-COOH.
2
Apart from glycine (R = H), the α-carbon is chiral, so they show optical isomerism; natural amino acids are the L-enantiomers.
3
In solution and as solids they exist as zwitterions, H3N+-CHR-COO-, which gives them high melting points and good water solubility.
4
In acid, the carboxylate is protonated, giving a cation; in alkali, the ammonium group loses H+, giving an anion.
5
The pH at which the amino acid is neutral overall is the isoelectric point.
6
They can be separated by electrophoresis or identified by chromatography with ninhydrin developer.

Section 2 of 13Proteins and peptide links

Amino acids join by condensation to form peptide (amide) links, -CONH-, with loss of water. Dipeptides, polypeptides and proteins are chains of amino acids. Proteins are hydrolysed by heating with 6 mol dm-3 HCl for about 24 hours (or by enzymes), giving a mixture of amino acids which can be separated by chromatography. Protein structure has levels:

Proteins and peptide links
Primary: the sequence of amino acids.
Secondary: α-helix or β-pleated sheet held by hydrogen bonds between the N-H and C=O of peptide links.
Tertiary: the 3D folding of the whole chain, held by hydrogen bonds, ionic interactions, disulfide bridges (S-S) and van der Waals forces between R groups.

Section 3 of 13Enzymes

Enzymes are protein catalysts with a specific active site whose shape is complementary to the substrate.

1
The substrate binds to form an enzyme–substrate complex, lowers the activation energy, and products leave.
2
Enzymes are stereospecific: they usually act on only one enantiomer of a chiral molecule.
3
Enzyme inhibitors (competitive) have a shape similar to the substrate and block the active site; many drugs work this way.
4
Denaturing by heat or extreme pH changes the tertiary structure and destroys activity.

Section 4 of 13Anticancer drugs: cisplatin

Cisplatin, cis-Pt(NH3)2Cl2, is a square planar platinum(II) complex.

Anticancer drugs: cisplatin
In the cell, the chloride ligands are replaced by water,
  • then the complex binds by ligand substitution to the nitrogen atoms of two adjacent guanine bases in DNA, preventing DNA replication,
  • so cancer cells cannot divide and die.
Only the cis isomer works, because the two binding sites must be next to one another.
Side effects include kidney damage and hair loss;
  • because cisplatin also affects healthy dividing cells, other drugs such as carboplatin and strategies for targeting delivery are used to reduce side effects.

Section 5 of 13Worked examples

  1. Draw the zwitterion of alanine. [1]1 mark

  2. Draw the dipeptide formed from glycine and alanine. [2]2 marks

  3. Explain why amino acids have high melting points. [2]2 marks

  4. Explain how cisplatin prevents cell division. [3]3 marks

Section 6 of 13Nucleotides and the DNA chain

The nucleic acid DNA is a polynucleotide, made up of many nucleotides bonded together in a long chain.

Nucleotides and the DNA chain
A nucleotide is a building block consisting of a phosphate group, 2-deoxyribose (a pentose sugar) and a nitrogenous base such as adenine, guanine, cytosine and thymine.
The base is attached to carbon 1 of the sugar and the phosphate to carbon 5.
  • Nucleotides are linked by condensation between the phosphate of one nucleotide and the sugar of the next,
  • forming a sugar–phosphate backbone with the bases pointing out.
This backbone has a repeating -sugar-phosphate- pattern.

Section 7 of 13The double helix and base pairing

DNA is made of two polynucleotide strands running in opposite directions, coiled into a double helix.

The double helix and base pairing
The strands are held together by hydrogen bonds between complementary bases: adenine pairs with thymine (two hydrogen bonds) and cytosine pairs with guanine (three hydrogen bonds).
The pairs are the right size (a purine with a pyrimidine) and have matching hydrogen-bonding groups (N-H and C=O or N donors/acceptors),
  • so only A-T and C-G fit.
Because of this, the amount of A equals T and C equals G in any sample.

Section 8 of 13Replication and the genetic code

When cells divide, the hydrogen bonds between the strands break (helicase), and each strand acts as a template for assembling complementary nucleotides (DNA polymerase), giving two identical molecules each containing one old and one new strand (semi-conservative replication).

Replication and the genetic code
The order of bases is the genetic code: each triplet of bases (a codon) codes for an amino acid; a gene is a sequence of triplets coding for a protein.
Mutations alter the base sequence and may change the protein produced.

Section 9 of 13DNA and drug action

Because cisplatin binds to guanine nitrogen atoms, it distorts the double helix and stops replication. Other anticancer drugs work by inhibiting enzymes needed for synthesis of DNA bases.

Section 10 of 13Hydrogen bonding and stability

Each hydrogen bond is weak, but the thousands along a DNA molecule together make the double helix very stable, while still allowing the strands to be separated during replication.

Hydrogen bonding and stability
The G-C pairs, with three hydrogen bonds, make regions of DNA richer in G and C more stable (a higher melting temperature) than A-T-rich regions.
The negatively charged phosphate groups on the outside of the helix make DNA soluble in water,
  • while the bases stacked inside are hydrophobic and are protected from the solvent.
In a drug context, small molecules that fit in the grooves of the helix or bind to bases can distort it and interfere with replication.

Section 11 of 13Worked examples

  1. Name the three components of a nucleotide in DNA. [3]3 marks

  2. A DNA sample has 30% adenine. State the percentage of the other bases. [3]3 marks

  3. Explain why adenine pairs only with thymine. [2]2 marks

  4. Describe how DNA replicates. [3]3 marks

Section 12 of 13Key terms

TermMeaning
ZwitterionIon with both a positive and a negative charge in the same molecule.
Peptide link-CONH- amide link between amino acids.
Isoelectric pointpH at which an amino acid has no net charge.
Active siteRegion of an enzyme where the substrate binds.
CisplatinPlatinum anticancer complex that binds to DNA.
TermMeaning
NucleotidePhosphate + sugar + nitrogenous base.
PolynucleotideChain of many nucleotides.
Complementary base pairingA-T and C-G bonding through hydrogen bonds.
Double helixTwo polynucleotide strands wound around each other.
CodonTriplet of bases coding for an amino acid.

Section 13 of 13Exam technique

1
Drawing a peptide link as -COON-.
2
Saying amino acids are all optically active (glycine is not).
3
Forgetting the zwitterion form in solution.
4
Saying a denatured enzyme loses its primary structure - the peptide bonds remain.
1
Saying A pairs with G.
2
Using ribose rather than deoxyribose.
3
Confusing hydrogen bonds between bases with covalent bonds in the backbone.
4
Saying DNA strands run in the same direction.

Last updated: